Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 3 of 59
Found at i:135197 original size:23 final size:24
Alignment explanation
Indices: 135152--135198 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
135142 AAAAATCATA
135152 GAATATTCTTTTCTTACTTACATGG
1 GAATATTCTTTTCTTAC-TACATGG
135177 GAATATTCTTCTTC-TAC-ACATG
1 GAATATTCTT-TTCTTACTACATG
135199 AAATAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (24 bp):
GAATATTCTTTTCTTACTACATGG
Found at i:138502 original size:2 final size:2
Alignment explanation
Indices: 138495--138532 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
138485 AATTCAACAT
138495 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
138533 AGGAGTAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:140332 original size:2 final size:2
Alignment explanation
Indices: 140318--140378 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
140308 NNNNNNNNNN
140318 TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
140358 TA TG TA TA TC TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
140379 CTACACGCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:152494 original size:2 final size:2
Alignment explanation
Indices: 152487--152530 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
152477 TATTTGCAGA
* *
152487 AT AT AT AT GT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
152529 AT
1 AT
152531 GAACCCAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154186 original size:2 final size:2
Alignment explanation
Indices: 154179--154247 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
154169 AGNACTACAC
* * *
154179 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
154221 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
154248 TTCTTTTACA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:155042 original size:2 final size:2
Alignment explanation
Indices: 155035--155063 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
155025 GAAGCAATAA
155035 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
155064 TTACACATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:163370 original size:2 final size:2
Alignment explanation
Indices: 163363--163395 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
163353 ACAAAAGACA
*
163363 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
163396 ATTGGCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:199068 original size:2 final size:2
Alignment explanation
Indices: 199061--199089 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
199051 GATGAGGGAG
199061 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
199090 TGTCATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:211145 original size:9 final size:9
Alignment explanation
Indices: 211131--211156 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
211121 ATTTCATGTC
211131 ATGCCTTTA
1 ATGCCTTTA
211140 ATGCCTTTA
1 ATGCCTTTA
211149 ATGCCTTT
1 ATGCCTTT
211157 TGTTTAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (9 bp):
ATGCCTTTA
Found at i:234950 original size:18 final size:18
Alignment explanation
Indices: 234923--234968 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
234913 TATCACGTAT
* * *
234923 ACACGTTTAAACATGATA
1 ACACGATTAAACACGAAA
234941 ACACGATTAAACACGAAA
1 ACACGATTAAACACGAAA
234959 ACACGATTAA
1 ACACGATTAA
234969 GTAAACGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.20
Consensus pattern (18 bp):
ACACGATTAAACACGAAA
Found at i:243770 original size:18 final size:17
Alignment explanation
Indices: 243727--243764 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
243717 TTATAAATTT
*
243727 AATT-CATACATAAAAA
1 AATTACATAAATAAAAA
243743 AATTACATAAATAAAATA
1 AATTACATAAATAAAA-A
243761 AATT
1 AATT
243765 GAATAAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTACATAAATAAAAA
Found at i:246145 original size:30 final size:30
Alignment explanation
Indices: 246087--246142 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
246077 TTTAGTTGAT
246087 TTAGGATTTATTTTCTTTATTTTATTTAAA
1 TTAGGATTTATTTTCTTTATTTTATTTAAA
*
246117 TTAGGA-TTCTTTT-TTTATTTTTATTT
1 TTAGGATTTATTTTCTTTA-TTTTATTT
246143 TAATACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 14 0.58
30 6 0.25
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.68
Consensus pattern (30 bp):
TTAGGATTTATTTTCTTTATTTTATTTAAA
Found at i:246505 original size:40 final size:40
Alignment explanation
Indices: 246450--246528 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
246440 TAGGCTATTT
**
246450 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTGA
*
246490 TTCACCTTAGTGGGGTTTTCAACCTCACCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTG
246529 TTTTTCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTGA
Found at i:249164 original size:40 final size:40
Alignment explanation
Indices: 249120--249198 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
249110 TTGGCTATTT
**
249120 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTGA
*
249160 TTCACCTTAGTGGGGTTTTCAACCTCACCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTG
249199 TTTTTCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTGA
Found at i:249346 original size:33 final size:33
Alignment explanation
Indices: 249308--249374 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
249298 ATCATAACAG
*
249308 AAACCACAATTAACCCTAGTGGCAT-GAGTCATA
1 AAACCACAATTAACCCTAGTAGCATGGA-TCATA
*
249341 AAACCATAATTAACCCTAGTAGCATGGATCATA
1 AAACCACAATTAACCCTAGTAGCATGGATCATA
249374 A
1 A
249375 GTATATCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.22
Consensus pattern (33 bp):
AAACCACAATTAACCCTAGTAGCATGGATCATA
Found at i:251078 original size:14 final size:15
Alignment explanation
Indices: 251061--251089 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
251051 CCTATCAAGC
251061 AAAT-TTTTTTATTT
1 AAATATTTTTTATTT
251075 AAATATTTTTTATTT
1 AAATATTTTTTATTT
251090 TTTATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
AAATATTTTTTATTT
Found at i:259033 original size:29 final size:29
Alignment explanation
Indices: 258999--259060 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 29
258989 GCCACAGAAC
258999 TTTATTTGCTTTCGGTGCAAATTCATTTG
1 TTTATTTGCTTTCGGTGCAAATTCATTTG
259028 TTTA-TTGCTTTCGGTGCAAATTCATTTG
1 TTTATTTGCTTTCGGTGCAAATTCATTTG
259056 TTTAT
1 TTTAT
259061 CTTCAATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (29 bp):
TTTATTTGCTTTCGGTGCAAATTCATTTG
Found at i:260465 original size:2 final size:2
Alignment explanation
Indices: 260439--260490 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
260429 GACATTGAGA
* * * *
260439 AT AT CT AT AT AA AT ACT AT AT -T AT AT AT AC AT AC AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
260481 AT AT AT AT AT
1 AT AT AT AT AT
260491 GGCATGAGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:260467 original size:18 final size:20
Alignment explanation
Indices: 260439--260487 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
260429 GACATTGAGA
*
260439 ATATCTATATAAATAC-TAT
1 ATATATATATAAATACATAT
*
260458 AT-TATATATACATACATAT
1 ATATATATATAAATACATAT
260477 ATATATATATA
1 ATATATATATA
260488 TATGGCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 8 0.31
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATATATAAATACATAT
Found at i:260600 original size:18 final size:18
Alignment explanation
Indices: 260568--260618 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
260558 ATTTAAGTCA
*
260568 TAATGAATAACAAACAAAT
1 TAAT-AATAATAAACAAAT
*
260587 TAATAATAATAAACAAGT
1 TAATAATAATAAACAAAT
260605 TAATTAATTAATAA
1 TAA-TAA-TAATAA
260619 CTAGTGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 15 0.54
19 7 0.25
20 6 0.21
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (18 bp):
TAATAATAATAAACAAAT
Found at i:260796 original size:4 final size:4
Alignment explanation
Indices: 260789--260815 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
260779 TTTCTCTTTC
260789 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
260816 CTCCCTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:270700 original size:24 final size:24
Alignment explanation
Indices: 270673--270729 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
270663 GCTCATAGCT
270673 TTATCAAATTTTACATGATAGTGC
1 TTATCAAATTTTACATGATAGTGC
270697 TTATCAAATTTTACATGATAGTGC
1 TTATCAAATTTTACATGATAGTGC
270721 TTATCAAAT
1 TTATCAAAT
270730 AATCTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (24 bp):
TTATCAAATTTTACATGATAGTGC
Found at i:275580 original size:5 final size:5
Alignment explanation
Indices: 275570--275594 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
275560 GGTAAAAATC
275570 TAGTT TAGTT TAGTT TAGTT TAGTT
1 TAGTT TAGTT TAGTT TAGTT TAGTT
275595 GCTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TAGTT
Found at i:284778 original size:2 final size:2
Alignment explanation
Indices: 284716--284764 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
284706 TTTGATCAAC
284716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
284758 AT CT AT A
1 AT AT AT A
284765 CTTACTACTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:285852 original size:5 final size:5
Alignment explanation
Indices: 285842--285873 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
285832 AAGCCACCAT
285842 TACTA TACTA TACTA TACTA TACTA TACTA TA
1 TACTA TACTA TACTA TACTA TACTA TACTA TA
285874 GTGACTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
TACTA
Found at i:299099 original size:15 final size:15
Alignment explanation
Indices: 299079--299110 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
299069 GGAAAAGGTT
299079 ATTTGTTTAGTAATA
1 ATTTGTTTAGTAATA
299094 ATTTGTTTAGTAATA
1 ATTTGTTTAGTAATA
299109 AT
1 AT
299111 ACAGTAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTTGTTTAGTAATA
Found at i:301988 original size:2 final size:2
Alignment explanation
Indices: 301981--302007 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
301971 CAATCACTCC
301981 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
302008 ATGATGGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:303701 original size:33 final size:33
Alignment explanation
Indices: 303659--303725 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
303649 TGTAAATACA
303659 TAGATTTTTCACATGATAATATATCTAGACATG
1 TAGATTTTTCACATGATAATATATCTAGACATG
303692 TAGATTTTTCACATGATAATATATCTAGACATG
1 TAGATTTTTCACATGATAATATATCTAGACATG
303725 T
1 T
303726 TCTTCCTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
TAGATTTTTCACATGATAATATATCTAGACATG
Found at i:335356 original size:18 final size:17
Alignment explanation
Indices: 335330--335363 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
335320 AAAAGTTATT
335330 ATAAAAATTTTATAAAAA
1 ATAAAAATTTT-TAAAAA
*
335348 ATAATAATTTTTAAAA
1 ATAAAAATTTTTAAAA
335364 TTAGACTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAATTTTTAAAAA
Found at i:338963 original size:35 final size:34
Alignment explanation
Indices: 338898--338967 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
338888 AGAATTGTCT
* *
338898 TGTGAATCCTGCTAATTAAGAAGTGTGGGAATCA
1 TGTGAATCCTGCTAACTAAGAAGTGCGGGAATCA
**
338932 TGTGAATCCTGCTAACCTGCGAAGTGCGGGAATCA
1 TGTGAATCCTGCTAA-CTAAGAAGTGCGGGAATCA
338967 T
1 T
338968 AGTCTAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (34 bp):
TGTGAATCCTGCTAACTAAGAAGTGCGGGAATCA
Found at i:339094 original size:22 final size:19
Alignment explanation
Indices: 339048--339097 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 19
339038 TTGGCTCTAG
339048 AAAGAAAGAAGAAGAAGGC
1 AAAGAAAGAAGAAGAAGGC
339067 AAAGAAAGAAGAAGAAGGC
1 AAAGAAAGAAGAAGAAGGC
339086 ATAAGAGAAGAA
1 A-AAGA-AAGAA
339098 AGCATAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 20 0.69
20 4 0.14
21 5 0.17
ACGTcount: A:0.64, C:0.04, G:0.30, T:0.02
Consensus pattern (19 bp):
AAAGAAAGAAGAAGAAGGC
Found at i:339113 original size:48 final size:48
Alignment explanation
Indices: 339061--339201 Score: 148
Period size: 48 Copynumber: 3.0 Consensus size: 48
339051 GAAAGAAGAA
* *
339061 GAAGGCAAAGAAAGAAGA-AG-AAGGCATAAGAGAAGAAAGCATAGGAAT
1 GAAGG-AAAGAAAGAAAAGAGTAAGG-AGAAGAGAAGAAAGCATAGGAAT
* * *
339109 GAAGGAAAAAAAAAAAAGAGTAAGGAGAGGAGAAGAAAGCATAGGAAT
1 GAAGGAAAGAAAGAAAAGAGTAAGGAGAAGAGAAGAAAGCATAGGAAT
* * * *
339157 GAAGG-AA-AAAG-AAAGAGTAAGTAGAGGAGAAGAAGGCTTAGGAAT
1 GAAGGAAAGAAAGAAAAGAGTAAGGAGAAGAGAAGAAAGCATAGGAAT
339202 AAGAGAGGCG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
45 31 0.38
46 3 0.04
47 11 0.13
48 33 0.40
49 4 0.05
ACGTcount: A:0.56, C:0.04, G:0.33, T:0.08
Consensus pattern (48 bp):
GAAGGAAAGAAAGAAAAGAGTAAGGAGAAGAGAAGAAAGCATAGGAAT
Found at i:339168 original size:24 final size:24
Alignment explanation
Indices: 339093--339171 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
339083 GGCATAAGAG
339093 AAGAAAGCATAGGAATGAAGGAAA
1 AAGAAAGCATAGGAATGAAGGAAA
* ** * * * *
339117 AAAAAAAAAGAGTAAGGAGAGG-AG
1 AAGAAAGCATAGGAATGA-AGGAAA
339141 AAGAAAGCATAGGAATGAAGGAAA
1 AAGAAAGCATAGGAATGAAGGAAA
339165 AAGAAAG
1 AAGAAAG
339172 AGTAAGTAGA
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
23 3 0.08
24 33 0.85
25 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.30, T:0.06
Consensus pattern (24 bp):
AAGAAAGCATAGGAATGAAGGAAA
Found at i:339183 original size:45 final size:46
Alignment explanation
Indices: 339090--339201 Score: 163
Period size: 45 Copynumber: 2.4 Consensus size: 46
339080 GAAGGCATAA
339090 GAGAAGAAAGCATAGGAATGAAGGAAAAAAAAAAAAGAGTAAGGAGAG
1 GAGAAGAAAGCATAGGAATGAAGG--AAAAAAAAAAGAGTAAGGAGAG
* *
339138 GAGAAGAAAGCATAGGAATGAAGG-AAAAAGAAAGAGTAAGTAGAG
1 GAGAAGAAAGCATAGGAATGAAGGAAAAAAAAAAGAGTAAGGAGAG
* *
339183 GAGAAGAAGGCTTAGGAAT
1 GAGAAGAAAGCATAGGAAT
339202 AAGAGAGGCG
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
45 36 0.60
48 24 0.40
ACGTcount: A:0.55, C:0.03, G:0.33, T:0.09
Consensus pattern (46 bp):
GAGAAGAAAGCATAGGAATGAAGGAAAAAAAAAAGAGTAAGGAGAG
Found at i:339715 original size:140 final size:140
Alignment explanation
Indices: 339463--339722 Score: 432
Period size: 140 Copynumber: 1.9 Consensus size: 140
339453 AGCGAGAAAT
*
339463 AACCAAGAAAGGTGCCTTGCCAAGGTTGAGAAACCGTGAAAAAAGGGTGTGGTGGTGGTGGAATC
1 AACCAAGAAAGGTGCCTTGCCAAGGTTGAGAAACCGTGAAAAAAGGGTGTGGTGGTAGTGGAATC
**
339528 AGGAAAGGATGTTGGAAATCAAATGGCACAGAAGAAGAACAATTGGATGGGAAGCAGAACCAGGA
66 AAAAAAGGATGTTGGAAATCAAATGGCACAGAAGAAGAACAATTGGATGGGAAGCAGAACCAGGA
339593 AAGCAAGGAG
131 AAGCAAGGAG
* *
339603 AACCAAGAAAGGTGCCTTGCCAAGGTTGAGAAATCGTGAAGAAAGGGTGTTGG-GGTAGTGGAAT
1 AACCAAGAAAGGTGCCTTGCCAAGGTTGAGAAACCGTGAAAAAAGGGTG-TGGTGGTAGTGGAAT
* * *
339667 CAAAAAAGGATGTTGGAATTCAAATGGTACAGAAGAAGAACAGTTGGATGGGAAGC
65 CAAAAAAGGATGTTGGAAATCAAATGGCACAGAAGAAGAACAATTGGATGGGAAGC
339723 GAGGGTAATA
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
140 108 0.97
141 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.34, T:0.17
Consensus pattern (140 bp):
AACCAAGAAAGGTGCCTTGCCAAGGTTGAGAAACCGTGAAAAAAGGGTGTGGTGGTAGTGGAATC
AAAAAAGGATGTTGGAAATCAAATGGCACAGAAGAAGAACAATTGGATGGGAAGCAGAACCAGGA
AAGCAAGGAG
Found at i:340400 original size:38 final size:38
Alignment explanation
Indices: 340349--340424 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
340339 CTTAACTTAG
340349 TCTACTGCAGCAATGGTTGAAGGATAAGAAAGAAATAC
1 TCTACTGCAGCAATGGTTGAAGGATAAGAAAGAAATAC
340387 TCTACTGCAGCAATGGTTGAAGGATAAGAAAGAAATAC
1 TCTACTGCAGCAATGGTTGAAGGATAAGAAAGAAATAC
340425 AATCTCCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (38 bp):
TCTACTGCAGCAATGGTTGAAGGATAAGAAAGAAATAC
Found at i:340644 original size:20 final size:21
Alignment explanation
Indices: 340619--340661 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
340609 AACACTTGTC
340619 AAGACATGGATT-CAAGTGTT
1 AAGACATGGATTACAAGTGTT
*
340639 AAGACATGGATTATAAGTGTT
1 AAGACATGGATTACAAGTGTT
340660 AA
1 AA
340662 AGGAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (21 bp):
AAGACATGGATTACAAGTGTT
Found at i:358485 original size:51 final size:51
Alignment explanation
Indices: 358407--358507 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 51
358397 TATTTTGGCG
* *
358407 ACTTGAACCATCAAATAGTTTTAGACACTT-ATCCATAATCTGC-AGAGCTA
1 ACTTGAACCATCAAATAGTTATAGACACTTAATCCAGAATCT-CTAGAGCTA
*
358457 ACTTGGACCATTCAAATAGCTTAT-GACACTTAATCCAGAATCTCTAGAGCT
1 ACTTGAACCA-TCAAATAG-TTATAGACACTTAATCCAGAATCTCTAGAGCT
358508 TACTAGCTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
50 9 0.20
51 16 0.36
52 19 0.43
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (51 bp):
ACTTGAACCATCAAATAGTTATAGACACTTAATCCAGAATCTCTAGAGCTA
Found at i:377861 original size:21 final size:21
Alignment explanation
Indices: 377820--377863 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
377810 ACTTAACCAA
* *
377820 TCTTTTTCCTCACCACCGATT
1 TCTTTATCCTCACCACAGATT
*
377841 TCTTTATCCTCACCATAGATT
1 TCTTTATCCTCACCACAGATT
377862 TC
1 TC
377864 CAAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.34, G:0.05, T:0.43
Consensus pattern (21 bp):
TCTTTATCCTCACCACAGATT
Found at i:382212 original size:37 final size:37
Alignment explanation
Indices: 382106--382197 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
382096 TTTCTGATAT
* * *
382106 ATTTCTGATTCATGCCACTAAGGTTAATTGTGGTTTTG
1 ATTT-TGACTCATGCCACCAAGGTTAATTGTGGTTTTC
382144 ATTTTGACTCATGCCACCAAGGTTAATTGTGG-TTTC
1 ATTTTGACTCATGCCACCAAGGTTAATTGTGGTTTTC
*
382180 ATTTTTGACTTATGCCAC
1 A-TTTTGACTCATGCCAC
382198 AGGGGTTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 4 0.08
37 41 0.84
38 4 0.08
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.42
Consensus pattern (37 bp):
ATTTTGACTCATGCCACCAAGGTTAATTGTGGTTTTC
Found at i:390292 original size:8 final size:8
Alignment explanation
Indices: 390279--390311 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
390269 CAATTAGTTT
390279 TTTATATA
1 TTTATATA
*
390287 TTTATACA
1 TTTATATA
390295 TTTATATA
1 TTTATATA
390303 TTTATATA
1 TTTATATA
390311 T
1 T
390312 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:390321 original size:20 final size:20
Alignment explanation
Indices: 390297--390344 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
390287 TTTATACATT
390297 TATATATTTATATATATTTTA
1 TATATATTTA-ATATATTTTA
* *
390318 -ATATATGTAATATTTTTTA
1 TATATATTTAATATATTTTA
390337 TATATATT
1 TATATATT
390345 AAGAAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATATTTAATATATTTTA
Found at i:392871 original size:205 final size:205
Alignment explanation
Indices: 392510--392879 Score: 614
Period size: 205 Copynumber: 1.8 Consensus size: 205
392500 AATTGTAGAA
* * * *
392510 ATATATTATATATACATATATTTAATTTATATATAAGCATTACTATAACTTATAATAGACTTTAT
1 ATATATTATATATACATATATTTAATTTATACATAAGCATTACTACAAATTATAATAAACTTTAT
* *
392575 TCATATGATTACACATGATAACTTTATTAGTTATCACCTTAGATTTTATAATATATTGTTTATAA
66 TCATATGATTACACATAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATAA
* *
392640 TTAGTTATTATTTATACAAGCTTTGATATAAAACACTTTAAAATGTAATTTGTATTATTAATTAT
131 TTAGTTATTATTTACACAAACTTTGATATAAAACACTTTAAAATGTAATTTGTATTATTAATTAT
392705 ATATAATGTC
196 ATATAATGTC
*
392715 ATATATTATATATACATATATTTAATTTATACATAAGTATTACTACAAATTATAATAAACTTTAT
1 ATATATTATATATACATATATTTAATTTATACATAAGCATTACTACAAATTATAATAAACTTTAT
* * * *
392780 TTATATGATTACGCTTAATAACTTTATTAGTTATCATCTTAGATTTTATAACATATTGTTTATAA
66 TCATATGATTACACATAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATAA
*
392845 TTAGTTATTATTTACATAAACTTTGATATAAAACA
131 TTAGTTATTATTTACACAAACTTTGATATAAAACA
392880 TTAAAACATA
Statistics
Matches: 151, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
205 151 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (205 bp):
ATATATTATATATACATATATTTAATTTATACATAAGCATTACTACAAATTATAATAAACTTTAT
TCATATGATTACACATAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATAA
TTAGTTATTATTTACACAAACTTTGATATAAAACACTTTAAAATGTAATTTGTATTATTAATTAT
ATATAATGTC
Found at i:413292 original size:74 final size:74
Alignment explanation
Indices: 413158--413298 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 74
413148 TAAATGAAAT
* * * ** *
413158 AAATCTTGCTAATAGTTATAATAAAAAATATTTCAACGATCTTCATTTGGTAAATGCATATCTAT
1 AAATCTTACTAATAATTATAATAAAAAATATTTCAACAATCTTCATTTAATAAATACATATCTAT
413223 AATAGGTTC
66 AATAGGTTC
* * *
413232 AAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATT-ATTTAATGAATACATATTTA
1 AAATCTTACTAATAATTATAATAAAAAATATTTCAACAATC-TTCATTTAATAAATACATATCTA
413296 TAA
65 TAA
413299 GTATAAGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 55 0.96
75 2 0.04
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (74 bp):
AAATCTTACTAATAATTATAATAAAAAATATTTCAACAATCTTCATTTAATAAATACATATCTAT
AATAGGTTC
Found at i:416422 original size:2 final size:2
Alignment explanation
Indices: 416415--416448 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
416405 ATAATCACTC
416415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
416449 CATCATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:423434 original size:12 final size:14
Alignment explanation
Indices: 423403--423441 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
423393 AGGAAGTTTG
423403 GAGAGAGAGAGACA
1 GAGAGAGAGAGACA
* *
423417 GAGAGAGAGAGTCG
1 GAGAGAGAGAGACA
*
423431 GAGAGAAAGAG
1 GAGAGAGAGAG
423442 GTGAATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.46, T:0.03
Consensus pattern (14 bp):
GAGAGAGAGAGACA
Found at i:427638 original size:77 final size:77
Alignment explanation
Indices: 427507--427660 Score: 272
Period size: 77 Copynumber: 2.0 Consensus size: 77
427497 ACTAGCTAGA
* *
427507 TTTAGTAAACACTTTTAATGATTGCATCAAAAACCCTTTTCTCTTCTTTGTCTTTCTTTTTTGTT
1 TTTAGTAAACACTTTTAATGATTGCATAAAAAACCATTTTCTCTTCTTTGTCTTTCTTTTTTGTT
427572 GGTTTTGGAAGC
66 GGTTTTGGAAGC
* *
427584 TTTAGTAAACACTTTTAATGATTGTATAAAAAACCATTTTCTCTTCTTTTTCTTTCTTTTTTGTT
1 TTTAGTAAACACTTTTAATGATTGCATAAAAAACCATTTTCTCTTCTTTGTCTTTCTTTTTTGTT
427649 GGTTTTGGAAGC
66 GGTTTTGGAAGC
427661 CATTGAAACT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (77 bp):
TTTAGTAAACACTTTTAATGATTGCATAAAAAACCATTTTCTCTTCTTTGTCTTTCTTTTTTGTT
GGTTTTGGAAGC
Found at i:435222 original size:2 final size:2
Alignment explanation
Indices: 435215--435266 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
435205 TGAGGAGGGC
* * *
435215 GA GA GA GA GA GA GA GA GA G- GA GG GA TA GTA -A NA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA
435256 GA GA GA GA GA G
1 GA GA GA GA GA G
435267 GGGGATATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.93
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.48, T:0.04
Consensus pattern (2 bp):
GA
Found at i:438359 original size:15 final size:15
Alignment explanation
Indices: 438333--438414 Score: 92
Period size: 15 Copynumber: 5.5 Consensus size: 15
438323 GTACGTTTAT
*
438333 TGGGAATGTGATTGC
1 TGGGAATATGATTGC
*
438348 TGGGTATATGATTGC
1 TGGGAATATGATTGC
* * *
438363 TAGAAATGTGATTGC
1 TGGGAATATGATTGC
*
438378 TGGGTATATGATTGC
1 TGGGAATATGATTGC
**
438393 TAAGAATATGATTGC
1 TGGGAATATGATTGC
438408 TGGGAAT
1 TGGGAAT
438415 TTAATTGTTA
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 52 1.00
ACGTcount: A:0.27, C:0.06, G:0.32, T:0.35
Consensus pattern (15 bp):
TGGGAATATGATTGC
Found at i:438371 original size:30 final size:30
Alignment explanation
Indices: 438336--438429 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
438326 CGTTTATTGG
438336 GAATGTGATTGCTGGGTATATGATTGCT-A
1 GAATGTGATTGCTGGGTATATGATTGCTAA
438365 GAAATGTGATTGCTGGGTATATGATTGCTAA
1 G-AATGTGATTGCTGGGTATATGATTGCTAA
* * * * *
438396 GAATATGATTGCTGGGAATTTAATTGTTAA
1 GAATGTGATTGCTGGGTATATGATTGCTAA
438426 GAAT
1 GAAT
438430 ATAATTTTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
29 1 0.02
30 55 0.95
31 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (30 bp):
GAATGTGATTGCTGGGTATATGATTGCTAA
Found at i:465331 original size:24 final size:24
Alignment explanation
Indices: 465304--465359 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
465294 TGTGGCTGGC
* *
465304 CCAAGGAAATCAAGTGTGAATTAT
1 CCAAGGAAATCAAGTGCGAATAAT
* * *
465328 CCAAGGAGATCAGGTGCGACTAAT
1 CCAAGGAAATCAAGTGCGAATAAT
465352 CCAAGGAA
1 CCAAGGAA
465360 GCATCAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (24 bp):
CCAAGGAAATCAAGTGCGAATAAT
Found at i:471462 original size:12 final size:13
Alignment explanation
Indices: 471447--471483 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
471437 TAAAGCTTTC
471447 ATATTA-TATTAT
1 ATATTATTATTAT
471459 ATA-TATTATTAT
1 ATATTATTATTAT
471471 -TATTATTATTAT
1 ATATTATTATTAT
471483 A
1 A
471484 AGGGTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTATTATTAT
Found at i:486908 original size:25 final size:26
Alignment explanation
Indices: 486874--486927 Score: 101
Period size: 25 Copynumber: 2.1 Consensus size: 26
486864 TTAGTCAATA
486874 TTTGAATTATATATTACAAATTCATT
1 TTTGAATTATATATTACAAATTCATT
486900 TTTG-ATTATATATTACAAATTCATT
1 TTTGAATTATATATTACAAATTCATT
486925 TTT
1 TTT
486928 CATGAACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (26 bp):
TTTGAATTATATATTACAAATTCATT
Found at i:491992 original size:29 final size:26
Alignment explanation
Indices: 491930--491993 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
491920 CAATTTTCAA
*
491930 TTATAATTTAATTATTTTTAGTTGTTT
1 TTATAA-TTAATTATTTTTAGTAGTTT
491957 TTATAATTAAGTTACTTTTTAGTGAGTTAT
1 TTATAATTAA-TTA-TTTTTAGT-AGTT-T
491987 TT-TAATT
1 TTATAATT
491994 TTATATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.12
27 9 0.28
28 8 0.25
29 8 0.25
30 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (26 bp):
TTATAATTAATTATTTTTAGTAGTTT
Found at i:492010 original size:24 final size:25
Alignment explanation
Indices: 491983--492036 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
491973 TTTTAGTGAG
491983 TTATTTTAATT-TTATATTATT-TTT
1 TTATTTTAATTATTAT-TTATTGTTT
*
492007 TTATTTTAGTTATTATTTATTGGTTT
1 TTATTTTAATTATTATTTATT-GTTT
492033 TTAT
1 TTAT
492037 ATTTTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 15 0.58
25 4 0.15
26 7 0.27
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (25 bp):
TTATTTTAATTATTATTTATTGTTT
Found at i:494973 original size:2 final size:2
Alignment explanation
Indices: 494966--495004 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
494956 AAGAGTTTAC
* *
494966 AT AT AT AT AT CT AT AT AT AT AT AT AT CT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
495005 TTGTCNATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:494987 original size:16 final size:16
Alignment explanation
Indices: 494966--495004 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
494956 AAGAGTTTAC
494966 ATATATATATCTATAT
1 ATATATATATCTATAT
494982 ATATATATATCTATAT
1 ATATATATATCTATAT
494998 ATA-ATAT
1 ATATATAT
495005 TTGTCNATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATATATCTATAT
Found at i:500552 original size:22 final size:22
Alignment explanation
Indices: 500533--500574 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
500523 CTTCGTTTTG
500533 CATTTTGTTTTCTTTTGTTTAT
1 CATTTTGTTTTCTTTTGTTTAT
* *
500555 CCTTTTGTTTTGTTTT-TTTA
1 CATTTTGTTTTCTTTTGTTTA
500575 CTTAGTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.74
Consensus pattern (22 bp):
CATTTTGTTTTCTTTTGTTTAT
Found at i:508487 original size:45 final size:42
Alignment explanation
Indices: 508419--508505 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 42
508409 ATAAATTCTG
508419 AAAGCATAATTTTTTTTTTCTTTTACATTTTAAGAGTAACCT
1 AAAGCATAATTTTTTTTTTCTTTTACATTTTAAGAGTAACCT
508461 NAAAGCCATAATTTTTTTTTTTCTTTTACATTTTAAGAGTAACCT
1 -AAAG-CATAA-TTTTTTTTTTCTTTTACATTTTAAGAGTAACCT
508506 TTAGATGCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
43 4 0.10
44 5 0.12
45 33 0.79
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.49
Consensus pattern (42 bp):
AAAGCATAATTTTTTTTTTCTTTTACATTTTAAGAGTAACCT
Found at i:518675 original size:26 final size:29
Alignment explanation
Indices: 518599--518684 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 29
518589 AATTATTTCA
*
518599 AATTTTTAATTCCATGCGAAGTGTAAATT
1 AATTTTTAATTCCTTGCGAAGTGTAAATT
*
518628 AATTTTTAATT-TTGTGCGAAGTGT-AA-T
1 AATTTTTAATTCCT-TGCGAAGTGTAAATT
* *
518655 -ATTTTTAATTCCTTGCAAAGTG-ATATT
1 AATTTTTAATTCCTTGCGAAGTGTAAATT
518682 AAT
1 AAT
518685 GCATTTTCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 19 0.40
27 3 0.06
28 4 0.09
29 21 0.45
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (29 bp):
AATTTTTAATTCCTTGCGAAGTGTAAATT
Found at i:519288 original size:20 final size:20
Alignment explanation
Indices: 519246--519323 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
519236 TTATTTTTTA
* *
519246 AATATTAATAATTTGTAATTT
1 AATATTAATAATTTATTA-TT
*
519267 AATTATT-ATATTTTATTATT
1 AA-TATTAATAATTTATTATT
519287 AATATTAATAATTTATT-TAT
1 AATATTAATAATTTATTAT-T
*
519307 AAT-TTAA-AAATTATTAT
1 AATATTAATAATTTATTAT
519324 GATTAAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.15
19 10 0.21
20 17 0.35
21 10 0.21
22 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
AATATTAATAATTTATTATT
Found at i:520007 original size:15 final size:15
Alignment explanation
Indices: 519975--520013 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
519965 CCTAAACTTA
*
519975 AAAATTAAT-ATTTT
1 AAAATTATTAATTTT
519989 -AAATTATTAATTTT
1 AAAATTATTAATTTT
520003 AAAATTATTAA
1 AAAATTATTAA
520014 GTAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 5 0.23
15 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATTATTAATTTT
Found at i:520398 original size:26 final size:26
Alignment explanation
Indices: 520369--520502 Score: 75
Period size: 27 Copynumber: 5.2 Consensus size: 26
520359 ATTCTACTGA
*
520369 TTAAATTATTAATAAAATATTAATAT
1 TTAAATAATTAATAAAATATTAATAT
*
520395 TT--A-AATT-ATCAAATATTAATAT
1 TTAAATAATTAATAAAATATTAATAT
*
520417 TTGAAATAAATT-ATAAAGTATTAATATT
1 TT-AAAT-AATTAATAAAATATTAATA-T
* * * *
520445 TTAAAAAAATAAAATAAAA-AATCATAT
1 TT-AAATAAT-TAATAAAATATTAATAT
* * *
520472 TTAAAT-TTTAAGTAAANTATTTATAT
1 TTAAATAATTAA-TAAAATATTAATAT
520498 TTAAA
1 TTAAA
520503 AAATAAAATT
Statistics
Matches: 82, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
22 16 0.20
23 3 0.04
24 3 0.04
25 6 0.07
26 16 0.20
27 22 0.27
28 11 0.13
29 5 0.06
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAATAATTAATAAAATATTAATAT
Found at i:520426 original size:27 final size:27
Alignment explanation
Indices: 520396--520454 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
520386 TATTAATATT
520396 TAAATTATCAAA-TATTAATATTTGAAA
1 TAAATTAT-AAAGTATTAATATTTGAAA
*
520423 TAAATTATAAAGTATTAATATTTTAAA
1 TAAATTATAAAGTATTAATATTTGAAA
*
520450 AAAAT
1 TAAAT
520455 AAAATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAATTATAAAGTATTAATATTTGAAA
Found at i:536661 original size:27 final size:27
Alignment explanation
Indices: 536623--536674 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
536613 TGGAGTAGTC
* *
536623 GCTCCGCGCCCTCAGATTCAGTCCCGT
1 GCTCCGAGCCCTCAGAATCAGTCCCGT
536650 GCTCCGAGCCCTCAGAATCAGTCCC
1 GCTCCGAGCCCTCAGAATCAGTCCC
536675 CCAATATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.44, G:0.21, T:0.19
Consensus pattern (27 bp):
GCTCCGAGCCCTCAGAATCAGTCCCGT
Found at i:536727 original size:21 final size:21
Alignment explanation
Indices: 536701--536740 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
536691 AAAGGAAAGC
536701 AAAAACAGGACAGGGTTAGCG
1 AAAAACAGGACAGGGTTAGCG
536722 AAAAACAGGACAGGGTTAG
1 AAAAACAGGACAGGGTTAG
536741 TGATAGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.33, T:0.10
Consensus pattern (21 bp):
AAAAACAGGACAGGGTTAGCG
Found at i:542669 original size:21 final size:21
Alignment explanation
Indices: 542643--542684 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
542633 CAAGACACAT
542643 GAAATGAAAGAAAGCATAAGA
1 GAAATGAAAGAAAGCATAAGA
*
542664 GAAATGAAAGAAAGCGTAAGA
1 GAAATGAAAGAAAGCATAAGA
542685 AAGATGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.26, T:0.10
Consensus pattern (21 bp):
GAAATGAAAGAAAGCATAAGA
Found at i:545275 original size:20 final size:20
Alignment explanation
Indices: 545250--545289 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
545240 AGACTCGAGC
545250 AAAATATCTATATTTTGCTT
1 AAAATATCTATATTTTGCTT
545270 AAAATATCTATATTTTGCTT
1 AAAATATCTATATTTTGCTT
545290 CTATAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (20 bp):
AAAATATCTATATTTTGCTT
Found at i:546957 original size:13 final size:13
Alignment explanation
Indices: 546939--546964 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
546929 TATAGTGCAA
546939 AGCATAATTTTGT
1 AGCATAATTTTGT
546952 AGCATAATTTTGT
1 AGCATAATTTTGT
546965 TTCGTCTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
AGCATAATTTTGT
Found at i:549928 original size:2 final size:2
Alignment explanation
Indices: 549921--550002 Score: 141
Period size: 2 Copynumber: 41.5 Consensus size: 2
549911 TTCGTACTTT
549921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
549963 TA TA TA TA TA TA TA TA TA TA TA TA TA NTA -A TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T
550003 CAAAATCAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.03
2 73 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:555430 original size:15 final size:15
Alignment explanation
Indices: 555384--555431 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
555374 TTAATAATAG
* *
555384 TTAATAAATTTTTAT
1 TTAATTAATTTTTAA
* * *
555399 TTGATTGATTATTAA
1 TTAATTAATTTTTAA
555414 TTAATTAATTTTTAA
1 TTAATTAATTTTTAA
555429 TTA
1 TTA
555432 TAAAAATTGA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TTAATTAATTTTTAA
Found at i:556129 original size:2 final size:2
Alignment explanation
Indices: 556122--556153 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
556112 TGTAACAAGG
556122 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
556154 CGTTTAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:564665 original size:6 final size:6
Alignment explanation
Indices: 564654--564678 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
564644 GAAAGGCATT
564654 GTCCGA GTCCGA GTCCGA GTCCGA G
1 GTCCGA GTCCGA GTCCGA GTCCGA G
564679 ATGTTTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GTCCGA
Found at i:566200 original size:2 final size:2
Alignment explanation
Indices: 566193--566218 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
566183 TGAGGATAAA
566193 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
566219 CACCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:568888 original size:21 final size:21
Alignment explanation
Indices: 568850--568889 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
568840 AGAATTCCTC
*
568850 AAAAAAATGCATTAAAATAAT
1 AAAAAAATGAATTAAAATAAT
* *
568871 AAAAAATTGAATTGAAATA
1 AAAAAAATGAATTAAAATA
568890 TTTCAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (21 bp):
AAAAAAATGAATTAAAATAAT
Found at i:573538 original size:227 final size:222
Alignment explanation
Indices: 573133--573554 Score: 558
Period size: 227 Copynumber: 1.9 Consensus size: 222
573123 ACGAATCCTG
* * **
573133 TTATTTAGTTTGATATAGCAATTATGATTAAAAATTGTAATTTAAAGTAATCGTGATCATAATTG
1 TTATTTAGTTTGATATAGCAATTATGATTAAAAATTGTAATTCAAAATAATAATGATCATAATTG
* * * ** *
573198 TAATTATAGATCTTGTGTTTGCGATTGAGAACAAATTTATTGTTATCAAGATTTTTGATCAGAAT
66 TAATTACAGATCTTATGTTTACGATTGAGAACAAATTTATTGCAATCAAGATTTTTAATCAGAAT
** * ** * *
573263 TTTATGTCTTACTTGATATTGCATTTATGATTACTTTTGACTATTGCAATCAAACGTAACTCAAT
131 TCCATGTCTTACTTGACATTGCATTTATGATTAAATTTGACCATTGCAATCAAACATAACTCAAT
573328 TGTAGATTAACCATTATCTTAATCATA
196 TGTAGATTAACCATTATCTTAATCATA
* *
573355 TTATTTAGTTTGTTATTA-CAATTATGATTAAAAATTGTAATTCAAAATAATAATGATCGTAATT
1 TTATTTAGTTTGATA-TAGCAATTATGATTAAAAATTGTAATTCAAAATAATAATGATCATAATT
* * * *
573419 GTAATTGCAGGCCTTTACTTATTTTTACGATTGAGAATAAATTTATTGCAATCAAGATTTTTAAT
65 GTAATTACA-G---AT-CTTATGTTTACGATTGAGAACAAATTTATTGCAATCAAGATTTTTAAT
* *
573484 CAGAATTCCATGTCTTACTTGACATTGCATTTATGATTAAATTTGGCCATTGCAATCAAACATAG
125 CAGAATTCCATGTCTTACTTGACATTGCATTTATGATTAAATTTGACCATTGCAATCAAACATAA
573549 CTCAAT
190 CTCAAT
573555 CCTAATGCTA
Statistics
Matches: 169, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
222 62 0.37
223 3 0.02
226 1 0.01
227 103 0.61
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (222 bp):
TTATTTAGTTTGATATAGCAATTATGATTAAAAATTGTAATTCAAAATAATAATGATCATAATTG
TAATTACAGATCTTATGTTTACGATTGAGAACAAATTTATTGCAATCAAGATTTTTAATCAGAAT
TCCATGTCTTACTTGACATTGCATTTATGATTAAATTTGACCATTGCAATCAAACATAACTCAAT
TGTAGATTAACCATTATCTTAATCATA
Found at i:577212 original size:33 final size:33
Alignment explanation
Indices: 577170--577235 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
577160 TTGGAATAAT
577170 AAAATATTAACAATAAATATTTTAGGTGATGCC
1 AAAATATTAACAATAAATATTTTAGGTGATGCC
*
577203 AAAATATTAATAATAAATATTTTAGGTGATGCC
1 AAAATATTAACAATAAATATTTTAGGTGATGCC
577236 CTCCATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (33 bp):
AAAATATTAACAATAAATATTTTAGGTGATGCC
Found at i:579709 original size:80 final size:80
Alignment explanation
Indices: 579636--580906 Score: 1539
Period size: 80 Copynumber: 15.9 Consensus size: 80
579626 TTTACAATAA
* *
579636 GAAATGATATTTCAATTATAATAAAATATAATTTATTATATTTTAGATCATTATTAATTTATTTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTTT
*** *
579701 AGGCATTTATAATAT
66 AAATATTTATAACAT
* * * * * *
579716 GAAATAATATTTAAATTCTAATAATATCTAATTTATTATATTTTAGAAAAATTATTAATTTGTTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTATATTTTAG-ATAATTATTAATTTATTT
579781 TAAATATTTATAACAT
65 TAAATATTTATAACAT
* * *
579797 GAAATTATATTTCAA-TACTAATAAAATGTAA-TTATTAAATTTTAGATAATTATTAATTTATTT
1 GAAATAATATTTCAATTA-TAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTT
* *
579860 TGAATATTTATAATAT
65 TAAATATTTATAACAT
* * * * **
579876 GAAATAAAATTTAAATTATAATAAAATATAATTTA-TATTATTTTATATAATTACTAATTTGCTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTA-TATTTTAGATAATTATTAATTTATTT
*
579940 TAAATACTTATAACAT
65 TAAATATTTATAACAT
* * * *
579956 GAAATAATATCTCAATTATAATAATATCTAATTTATTATATTTTAGAAAATTATTAATTTATTTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTTT
580021 AAATATTTATAACAT
66 AAATATTTATAACAT
* * *
580036 GAAATTATATTTCAA-TACTAATAAAATGTAA-TTATTAAATTTTAGATAATTATTAATTTATTT
1 GAAATAATATTTCAATTA-TAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTT
* *
580099 TGAATATTTATAATAT
65 TAAATATTTATAACAT
* * * * **
580115 GAAATAAAATTTAAATTATAATAAAATATAATTTA-TATTATTTTATATAATTACTAATTTGCTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTA-TATTTTAGATAATTATTAATTTATTT
*
580179 TAAATACTTATAACAT
65 TAAATATTTATAACAT
* * * *
580195 GAAATAATATCTCAATTATAATAATATCTAATTTATTATATTTTAGAAAATTATTAATTTATTTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTTT
580260 AAATATTTATAACAT
66 AAATATTTATAACAT
* * *
580275 GAAATTATATTTCAA-TACTAATAAAATGTAA-TTATTAAATTTTAGATAATTATTAATTTATTT
1 GAAATAATATTTCAATTA-TAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTT
* *
580338 TGAATATTTATAATAT
65 TAAATATTTATAACAT
* * * * **
580354 GAAATAAAATTTAAATTATAATAAAATATAATTTA-TATTATTTTATATAATTACTAATTTGCTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTA-TATTTTAGATAATTATTAATTTATTT
*
580418 TAAATACTTATAACAT
65 TAAATATTTATAACAT
* * * *
580434 GAAATAATATCTCAATTATAATAATATCTAATTTATTATATTTTAGAAAATTATTAATTTATTTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTTT
580499 AAATATTTATAACAT
66 AAATATTTATAACAT
* * *
580514 GAAATTATATTTCAA-TACTAATAAAATGTAA-TTATTAAATTTTAGATAATTATTAATTTATTT
1 GAAATAATATTTCAATTA-TAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTT
* *
580577 TGAATATTTATAATAT
65 TAAATATTTATAACAT
* * * * **
580593 GAAATAAAATTTAAATTATAATAAAATATAATTTA-TATTATTTTATATAATTACTAATTTGCTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTA-TATTTTAGATAATTATTAATTTATTT
*
580657 TAAATACTTATAACAT
65 TAAATATTTATAACAT
* * * *
580673 GAAATAATATCTCAATTATAATAATATCTAATTTATTATATTTTAGAAAATTATTAATTTATTTT
1 GAAATAATATTTCAATTATAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTTT
580738 AAATATTTATAACAT
66 AAATATTTATAACAT
* * * * *
580753 GAAATTATATTTCAA-TACTAATGAAATCTAA-TTATTATATTTTAGAAAATTATTAATTTACTT
1 GAAATAATATTTCAATTA-TAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTT
* *
580816 GAAATATTTATAATAT
65 TAAATATTTATAACAT
* * *
580832 GAAATAATATTTCAATTATAATAAAATCA-AATTTA-TATCTTTTTGGTAAATTATTAATTTATT
1 GAAATAATATTTCAATTATAATAAAAT-ATAATTTATTATATTTTAGAT-AATTATTAATTTATT
*
580895 TTTAATATTTAT
64 TTAAATATTTAT
580907 TATATTTTAA
Statistics
Matches: 1010, Mismatches: 155, Indels: 52
0.83 0.13 0.04
Matches are distributed among these distances:
79 351 0.35
80 600 0.59
81 59 0.06
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (80 bp):
GAAATAATATTTCAATTATAATAAAATATAATTTATTATATTTTAGATAATTATTAATTTATTTT
AAATATTTATAACAT
Found at i:579900 original size:17 final size:17
Alignment explanation
Indices: 579878--579912 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
579868 TATAATATGA
*
579878 AATAAAATTTAAATTAT
1 AATAAAATATAAATTAT
*
579895 AATAAAATATAATTTAT
1 AATAAAATATAAATTAT
579912 A
1 A
579913 TTATTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAAATATAAATTAT
Found at i:579908 original size:22 final size:23
Alignment explanation
Indices: 579867--579916 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
579857 TTTTGAATAT
579867 TTATAATATGAAATAAAATTTAAA
1 TTATAATA-GAAATAAAATTTAAA
* *
579891 TTATAATA-AAATATAATTTATA
1 TTATAATAGAAATAAAATTTAAA
579913 TTAT
1 TTAT
579917 TTTATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
24 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATAATAGAAATAAAATTTAAA
Found at i:580052 original size:27 final size:26
Alignment explanation
Indices: 580014--580071 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
580004 AATTATTAAT
* * *
580014 TTATTTTAAATATTTATAACATGAAA
1 TTATTTTAAATACTAATAAAATGAAA
* *
580040 TTATATTTCAATACTAATAAAATGTAA
1 TTAT-TTTAAATACTAATAAAATGAAA
580067 TTATT
1 TTATT
580072 AAATTTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (26 bp):
TTATTTTAAATACTAATAAAATGAAA
Found at i:580076 original size:239 final size:239
Alignment explanation
Indices: 579624--580869 Score: 2201
Period size: 239 Copynumber: 5.2 Consensus size: 239
579614 AGTATTATTT
* * * * * * *
579624 TATTTACAATAAGAAATGATATTTCAATTATAATAAAATATAATTTAT-TATATTTTAGATCATT
1 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATAT-TATTTTATATAATT
* ** *** * * * * *
579688 ATTAATTTATTTTAGGCATTTATAATATGAAATAATATTTAAATTCTAATAATATCTAATTTATT
65 ACTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATT
*
579753 ATATTTTAGAAAAATTATTAATTTGTTTTAAATATTTATAACATGAAATTATATTTCAATACTAA
130 ATATTTTAG-AAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAA
579818 TAAAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
194 TAAAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
579864 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
1 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
579929 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
66 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
579994 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
131 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
580059 AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
196 AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
580103 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
1 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
580168 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
66 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
580233 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
131 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
580298 AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
196 AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
580342 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
1 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
580407 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
66 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
580472 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
131 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
580537 AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
196 AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
580581 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
1 TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
580646 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
66 CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
*
580711 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATG
131 TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
* * * *
580776 AAATCTAATTATTATATTTTAGAAAATTATTAATTTA-CTTGAAA
196 AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTG-AA
* *
580820 TATTTATAATATGAAATAATATTTCAATTATAATAAAATCA-AATTTATAT
1 TATTTATAATATGAAATAAAATTTAAATTATAATAAAAT-ATAATTTATAT
580870 CTTTTTGGTA
Statistics
Matches: 977, Mismatches: 26, Indels: 7
0.97 0.03 0.01
Matches are distributed among these distances:
238 3 0.00
239 854 0.87
240 119 0.12
241 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (239 bp):
TATTTATAATATGAAATAAAATTTAAATTATAATAAAATATAATTTATATTATTTTATATAATTA
CTAATTTGCTTTAAATACTTATAACATGAAATAATATCTCAATTATAATAATATCTAATTTATTA
TATTTTAGAAAATTATTAATTTATTTTAAATATTTATAACATGAAATTATATTTCAATACTAATA
AAATGTAATTATTAAATTTTAGATAATTATTAATTTATTTTGAA
Found at i:580139 original size:17 final size:17
Alignment explanation
Indices: 580117--580151 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
580107 TATAATATGA
*
580117 AATAAAATTTAAATTAT
1 AATAAAATATAAATTAT
*
580134 AATAAAATATAATTTAT
1 AATAAAATATAAATTAT
580151 A
1 A
580152 TTATTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAAATATAAATTAT
Found at i:580147 original size:22 final size:23
Alignment explanation
Indices: 580106--580155 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
580096 TTTTGAATAT
580106 TTATAATATGAAATAAAATTTAAA
1 TTATAATA-GAAATAAAATTTAAA
* *
580130 TTATAATA-AAATATAATTTATA
1 TTATAATAGAAATAAAATTTAAA
580152 TTAT
1 TTAT
580156 TTTATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
24 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATAATAGAAATAAAATTTAAA
Found at i:580291 original size:27 final size:26
Alignment explanation
Indices: 580253--580310 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
580243 AATTATTAAT
* * *
580253 TTATTTTAAATATTTATAACATGAAA
1 TTATTTTAAATACTAATAAAATGAAA
* *
580279 TTATATTTCAATACTAATAAAATGTAA
1 TTAT-TTTAAATACTAATAAAATGAAA
580306 TTATT
1 TTATT
580311 AAATTTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (26 bp):
TTATTTTAAATACTAATAAAATGAAA
Found at i:580378 original size:17 final size:17
Alignment explanation
Indices: 580356--580390 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
580346 TATAATATGA
*
580356 AATAAAATTTAAATTAT
1 AATAAAATATAAATTAT
*
580373 AATAAAATATAATTTAT
1 AATAAAATATAAATTAT
580390 A
1 A
580391 TTATTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAAATATAAATTAT
Found at i:580386 original size:22 final size:23
Alignment explanation
Indices: 580345--580394 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
580335 TTTTGAATAT
580345 TTATAATATGAAATAAAATTTAAA
1 TTATAATA-GAAATAAAATTTAAA
* *
580369 TTATAATA-AAATATAATTTATA
1 TTATAATAGAAATAAAATTTAAA
580391 TTAT
1 TTAT
580395 TTTATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
24 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATAATAGAAATAAAATTTAAA
Found at i:580530 original size:27 final size:26
Alignment explanation
Indices: 580492--580549 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
580482 AATTATTAAT
* * *
580492 TTATTTTAAATATTTATAACATGAAA
1 TTATTTTAAATACTAATAAAATGAAA
* *
580518 TTATATTTCAATACTAATAAAATGTAA
1 TTAT-TTTAAATACTAATAAAATGAAA
580545 TTATT
1 TTATT
580550 AAATTTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (26 bp):
TTATTTTAAATACTAATAAAATGAAA
Found at i:580617 original size:17 final size:17
Alignment explanation
Indices: 580595--580629 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
580585 TATAATATGA
*
580595 AATAAAATTTAAATTAT
1 AATAAAATATAAATTAT
*
580612 AATAAAATATAATTTAT
1 AATAAAATATAAATTAT
580629 A
1 A
580630 TTATTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAAATATAAATTAT
Found at i:580625 original size:22 final size:23
Alignment explanation
Indices: 580584--580633 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
580574 TTTTGAATAT
580584 TTATAATATGAAATAAAATTTAAA
1 TTATAATA-GAAATAAAATTTAAA
* *
580608 TTATAATA-AAATATAATTTATA
1 TTATAATAGAAATAAAATTTAAA
580630 TTAT
1 TTAT
580634 TTTATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
24 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATAATAGAAATAAAATTTAAA
Found at i:580906 original size:21 final size:21
Alignment explanation
Indices: 580882--580945 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
580872 TTTTGGTAAA
*
580882 TTATTAATTTATTTTTAATAT
1 TTATTAATTTATTTTAAATAT
*
580903 TTATT-A--TATTTTAAATAA
1 TTATTAATTTATTTTAAATAT
*
580921 TTATTAGTTTATTTTAAATAT
1 TTATTAATTTATTTTAAATAT
580942 TTAT
1 TTAT
580946 GATATGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 15 0.42
20 1 0.03
21 20 0.56
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATTAATTTATTTTAAATAT
Found at i:580914 original size:18 final size:18
Alignment explanation
Indices: 580878--580950 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
580868 ATCTTTTTGG
*
580878 TAAATTATTAATT-TATTT
1 TAAA-TATTTATTATATTT
*
580896 TTAATATTTATTATATTT
1 TAAATATTTATTATATTT
*
580914 TAAATAATTATTAGTTTATTT
1 TAAATATTTATTA---TATTT
*
580935 TAAATATTTATGATAT
1 TAAATATTTATTATAT
580951 GAAATAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
17 7 0.16
18 22 0.49
21 16 0.36
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TAAATATTTATTATATTT
Found at i:580985 original size:80 final size:75
Alignment explanation
Indices: 580901--581111 Score: 248
Period size: 73 Copynumber: 2.8 Consensus size: 75
580891 TATTTTTAAT
* * *
580901 ATTTATTATATTTTAAATAATTATTAGTTTATTTTAAATATTTATGATATGAAATAATATTTCAA
1 ATTTATTATATTTTAAATAATTATTAATTTATTTTAAATATTTATAAGATGAAATAATA--T--A
580966 TTATAATAAAATCTA
62 TT-TAATAAAATCTA
* * *
580981 ATTTATTATATTTTAAATAATTGTCAATTTATTTTAAATATTTGTAAGATGAAAT-A-ATATTTA
1 ATTTATTATATTTTAAATAATTATTAATTTATTTTAAATATTTATAAGATGAAATAATATATTTA
*
581044 ATAAAATGTA
66 ATAAAATCTA
* ** *
581054 ATTTATT-TAAATTTGGATAATTACTAATTTATTTTAAATATTTATAAGATGAAATAAT
1 ATTTATTAT-ATTTTAAATAATTATTAATTTATTTTAAATATTTATAAGATGAAATAAT
581112 GTTATTTATA
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
72 1 0.01
73 57 0.50
74 4 0.04
76 1 0.01
78 1 0.01
79 1 0.01
80 49 0.43
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.49
Consensus pattern (75 bp):
ATTTATTATATTTTAAATAATTATTAATTTATTTTAAATATTTATAAGATGAAATAATATATTTA
ATAAAATCTA
Found at i:581010 original size:119 final size:119
Alignment explanation
Indices: 580784--581023 Score: 340
Period size: 119 Copynumber: 2.0 Consensus size: 119
580774 TGAAATCTAA
580784 TTATTATATTTTAGAAAATTATTAATTTACTTGAAATATTTATAATATGAAATAATATTTCAATT
1 TTATTATATTTTAGAAAATTATTAATTTACTTGAAATATTTATAATATGAAATAATATTTCAATT
* *** * *
580849 ATAATAAAATCAAATTTATATCTTTTTGGTAAATTATTAATTTATTTTTAATAT
66 ATAATAAAATCAAATTTATATATTTTAAATAAATTATCAATTTATTTTAAATAT
* * * *
580903 TTATTATATTTTA-AATAATTATTAGTTTATTTTAAATATTTATGATATGAAATAATATTTCAAT
1 TTATTATATTTTAGAA-AATTATTAATTTACTTGAAATATTTATAATATGAAATAATATTTCAAT
* *
580967 TATAATAAAATCTAATTTATTATATTTTAAAT-AATTGTCAATTTATTTTAAATAT
65 TATAATAAAATCAAATTTA-TATATTTTAAATAAATTATCAATTTATTTTAAATAT
581022 TT
1 TT
581024 GTAAGATGAA
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
118 2 0.02
119 97 0.91
120 8 0.07
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (119 bp):
TTATTATATTTTAGAAAATTATTAATTTACTTGAAATATTTATAATATGAAATAATATTTCAATT
ATAATAAAATCAAATTTATATATTTTAAATAAATTATCAATTTATTTTAAATAT
Found at i:581298 original size:26 final size:26
Alignment explanation
Indices: 581260--581316 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
581250 TTATATTTTA
* *
581260 ATTATATTTTCTATAATTTTTAATTT
1 ATTATATTGTCTATAAATTTTAATTT
581286 ATTATATTGTCTATAAATTTTAATTT
1 ATTATATTGTCTATAAATTTTAATTT
581312 ATTAT
1 ATTAT
581317 TTTGCATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTATATTGTCTATAAATTTTAATTT
Found at i:581737 original size:21 final size:22
Alignment explanation
Indices: 581689--581737 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
581679 CTAACAGTAA
* *
581689 AATAATAAATTAATACTATATT
1 AATATTAAATTAATACTATATG
* *
581711 AGTATTAAATT-ATATTATATG
1 AATATTAAATTAATACTATATG
581732 AATATT
1 AATATT
581738 TATATGTGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
AATATTAAATTAATACTATATG
Found at i:589376 original size:15 final size:15
Alignment explanation
Indices: 589347--589375 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
589337 TGGTTTAATT
589347 TTTTTAATTTAAAAA
1 TTTTTAATTTAAAAA
589362 TTTTT-ATTTAAAAA
1 TTTTTAATTTAAAAA
589376 AATAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTAATTTAAAAA
Found at i:595986 original size:17 final size:17
Alignment explanation
Indices: 595947--595989 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
595937 GTTCTGTAAG
595947 TTTTTTCTTTTTCTTTC
1 TTTTTTCTTTTTCTTTC
**
595964 CCTTTTCTTTTTCTTAT-
1 TTTTTTCTTTTTCTT-TC
595981 TTTTTTCTT
1 TTTTTTCTT
595990 GCTCTAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTTC
Found at i:603956 original size:27 final size:30
Alignment explanation
Indices: 603900--603956 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 30
603890 ACAGTTAGGC
*
603900 AAATCTCTTCATTTATTTAAAAATTCAAAT
1 AAATCTCTTCATTTATTTAAAAAGTCAAAT
603930 AAATCT-TT-ATTT-TTTATAAAAGT-AAAT
1 AAATCTCTTCATTTATTTA-AAAAGTCAAAT
603957 CGAAATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 8 0.32
28 9 0.36
29 2 0.08
30 6 0.24
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (30 bp):
AAATCTCTTCATTTATTTAAAAAGTCAAAT
Found at i:613164 original size:26 final size:26
Alignment explanation
Indices: 613134--613184 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
613124 GCACTTGATC
613134 AATGAGACAATTCATAATCAATGTGG
1 AATGAGACAATTCATAATCAATGTGG
* *
613160 AATGAGACAATTCGTATTCAATGTG
1 AATGAGACAATTCATAATCAATGTG
613185 AGTCGTTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (26 bp):
AATGAGACAATTCATAATCAATGTGG
Found at i:613876 original size:2 final size:2
Alignment explanation
Indices: 613864--613907 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
613854 TTCTTTTGAA
* * * *
613864 AT AT GT AT AT AT AC AT AT AT TT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
613906 AT
1 AT
613908 TCTTGCAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:614641 original size:36 final size:37
Alignment explanation
Indices: 614584--614658 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 37
614574 CTAGCAACCA
* *
614584 AGGACATGCCCCAAGGTTCAG-CCAGGAACCAAGGCT
1 AGGACATGCACCAAGGTTCAGCCCAGGAACCAAGCCT
* *
614620 AGGATATGCACCAAGGTTCAGCCCAGGAATCAAGCCT
1 AGGACATGCACCAAGGTTCAGCCCAGGAACCAAGCCT
614657 AG
1 AG
614659 AACAAGCCGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 19 0.56
37 15 0.44
ACGTcount: A:0.32, C:0.28, G:0.27, T:0.13
Consensus pattern (37 bp):
AGGACATGCACCAAGGTTCAGCCCAGGAACCAAGCCT
Found at i:630928 original size:125 final size:127
Alignment explanation
Indices: 630691--630943 Score: 377
Period size: 125 Copynumber: 2.0 Consensus size: 127
630681 CAACATTCCA
* *
630691 ATATTAAAAGTTTTTTGATATACGATAAGGGTAATGCTAATCGTGGTAATTATTGGGCAACATGG
1 ATATTAAAAGTTTTTTGATAAACGATAAGGGTAATGCTAATCGTGGTAATTACTGGGCAACATGG
* * *
630756 CAACATTCAGATAGACACATATGATAGGTTCAGGTTGGGTTCAAGGTAATGCTAATGGTGGT
66 CAACATTCAAACAGACACATATGATAGGTTCAGGTTGGGTTCAAGGTAATGCCAATGGTGGT
* *
630818 ATATTAAAAG-TTTTTGATAAATGATAAGGGTAATGCTAATGGTGGTAATTACT-GGCAACATGG
1 ATATTAAAAGTTTTTTGATAAACGATAAGGGTAATGCTAATCGTGGTAATTACTGGGCAACATGG
* * * *
630881 CAACATTCAAACAGAGACATTTGATAGGTTC-GGATTTGGTTCGAGGTAATGCCAATGGTGGT
66 CAACATTCAAACAGACACATATGATAGGTTCAGG-TTGGGTTCAAGGTAATGCCAATGGTGGT
630943 A
1 A
630944 AGTAGTGGTG
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
124 2 0.02
125 63 0.55
126 39 0.34
127 10 0.09
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (127 bp):
ATATTAAAAGTTTTTTGATAAACGATAAGGGTAATGCTAATCGTGGTAATTACTGGGCAACATGG
CAACATTCAAACAGACACATATGATAGGTTCAGGTTGGGTTCAAGGTAATGCCAATGGTGGT
Found at i:635051 original size:14 final size:14
Alignment explanation
Indices: 635032--635065 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
635022 TTCCTCATCC
*
635032 GATTTACGATTTAG
1 GATTTACGAGTTAG
635046 GATTTACGAGTTAG
1 GATTTACGAGTTAG
*
635060 GGTTTA
1 GATTTA
635066 TTTATGTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.41
Consensus pattern (14 bp):
GATTTACGAGTTAG
Found at i:642583 original size:2 final size:2
Alignment explanation
Indices: 642576--642608 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
642566 AAAAACCAAT
*
642576 TA TA TA TA TA TA TA TA TA TA TA CA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
642609 ATACATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:642612 original size:14 final size:14
Alignment explanation
Indices: 642574--642618 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
642564 ACAAAAACCA
*
642574 ATTATAT-ATATAT
1 ATTATATAATACAT
642587 A-TATATATATACAT
1 ATTATATA-ATACAT
642601 ATTATATAATACAT
1 ATTATATAATACAT
642615 ATTA
1 ATTA
642619 ATTTCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 1 0.04
14 16 0.57
15 6 0.21
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATATAATACAT
Found at i:644141 original size:19 final size:20
Alignment explanation
Indices: 644117--644156 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
644107 GTTTCAATTA
*
644117 TTTTTTAATTT-TTTAC-TT
1 TTTTTTTATTTATTTACGTT
644135 TTTTTTTATTTATTTACGTT
1 TTTTTTTATTTATTTACGTT
644155 TT
1 TT
644157 GTATAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTTTTATTTATTTACGTT
Found at i:649707 original size:21 final size:21
Alignment explanation
Indices: 649681--649732 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
649671 TCAAATGCTT
649681 GGTGCAAATAACTTGTATATG
1 GGTGCAAATAACTTGTATATG
649702 GGTGCAAATAACTTGTATATG
1 GGTGCAAATAACTTGTATATG
*
649723 AGT-CAAATAA
1 GGTGCAAATAA
649733 TCGGTGCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (21 bp):
GGTGCAAATAACTTGTATATG
Found at i:652015 original size:85 final size:83
Alignment explanation
Indices: 651827--652027 Score: 192
Period size: 85 Copynumber: 2.4 Consensus size: 83
651817 AATATTGAAA
* * * *
651827 ATATTAATCCCTGTCTATAGACACTTGTTAACAAGACCATTAATCCATGTTTACATACACTTATT
1 ATATTAATCCATGT-TATAGACACTTGTT-A-AAGAACACTAATCCATGTCTACATACACTTATT
* *
651892 ATTGTTATTTTAGTTTAAGAT
63 ATTGTTATTTTAGTTGAAAAT
* ** * * **
651913 -CATTAATCTGTGTTTATAGACGCTTGTT-AAGAACACTAATCCCTGTCTACATATGCTTATTAT
1 ATATTAATCCATG-TTATAGACACTTGTTAAAGAACACTAATCCATGTCTACATACACTTATTAT
651976 TGTTATTTTAGTATCGAAAAT
65 TGTTATTTTAGT-T-GAAAAT
651997 ATATTAATCCATGCTTATAGACA-TTCGTTAA
1 ATATTAATCCATG-TTATAGACACTT-GTTAA
652028 GAATTTCAGA
Statistics
Matches: 92, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
82 41 0.45
83 1 0.01
84 6 0.07
85 42 0.46
86 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (83 bp):
ATATTAATCCATGTTATAGACACTTGTTAAAGAACACTAATCCATGTCTACATACACTTATTATT
GTTATTTTAGTTGAAAAT
Found at i:652623 original size:7 final size:7
Alignment explanation
Indices: 652587--652636 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
652577 GTCCATGAAA
652587 CTGGCTG
1 CTGGCTG
*
652594 CGGGCTG
1 CTGGCTG
*
652601 CGGGCTG
1 CTGGCTG
652608 CTGGCTG
1 CTGGCTG
652615 CTGGCTG
1 CTGGCTG
*
652622 CTGGGTG
1 CTGGCTG
*
652629 CTGTCTG
1 CTGGCTG
652636 C
1 C
652637 ACTCTCACGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.00, C:0.28, G:0.46, T:0.26
Consensus pattern (7 bp):
CTGGCTG
Found at i:666904 original size:2 final size:2
Alignment explanation
Indices: 666897--666926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
666887 CACTTCATAA
666897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
666927 GATAAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:682675 original size:13 final size:12
Alignment explanation
Indices: 682645--682678 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
682635 CCTTATACTA
*
682645 TTTTTAAAATAT
1 TTTTTAATATAT
682657 TTTTTAATATAT
1 TTTTTAATATAT
682669 TTATTTAATA
1 TT-TTTAATA
682679 ATAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTAATATAT
Found at i:683427 original size:2 final size:2
Alignment explanation
Indices: 683420--683490 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
683410 TGTTTTGATA
** *
683420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GN GT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
683461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
683491 GATAGAACCT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:688263 original size:39 final size:39
Alignment explanation
Indices: 688214--688367 Score: 209
Period size: 39 Copynumber: 3.9 Consensus size: 39
688204 ATGCACAAGC
*
688214 TCCTGAATGTTTCAACAGGGTCGATTGCCCCATGCATAT
1 TCCTGAATGTTTCAACAGGGTCGAATGCCCCATGCATAT
*
688253 TCCTGAATGTTTCAACAGGGTCGAATGCCCCATGCACGCTAA
1 TCCTGAATGTTTCAACAGGGTCGAATGCCCCATGCA---TAT
* * *
688295 TCCTGAATGTTTCAACAGGGTCAAATGCCCCATGCGTGT
1 TCCTGAATGTTTCAACAGGGTCGAATGCCCCATGCATAT
* * *
688334 TCCTGAACGTTTCAACATGGTCGATTGCCCCATG
1 TCCTGAATGTTTCAACAGGGTCGAATGCCCCATG
688368 TATAAAGGAC
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
39 66 0.65
42 36 0.35
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (39 bp):
TCCTGAATGTTTCAACAGGGTCGAATGCCCCATGCATAT
Found at i:688307 original size:81 final size:81
Alignment explanation
Indices: 688214--688367 Score: 245
Period size: 81 Copynumber: 1.9 Consensus size: 81
688204 ATGCACAAGC
* * *
688214 TCCTGAATGTTTCAACAGGGTCGATTGCCCCATGCATATTCCTGAATGTTTCAACAGGGTCGAAT
1 TCCTGAATGTTTCAACAGGGTCAAATGCCCCATGCATATTCCTGAACGTTTCAACAGGGTCGAAT
688279 GCCCCATGCACGCTAA
66 GCCCCATGCACGCTAA
* * * *
688295 TCCTGAATGTTTCAACAGGGTCAAATGCCCCATGCGTGTTCCTGAACGTTTCAACATGGTCGATT
1 TCCTGAATGTTTCAACAGGGTCAAATGCCCCATGCATATTCCTGAACGTTTCAACAGGGTCGAAT
688360 GCCCCATG
66 GCCCCATG
688368 TATAAAGGAC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (81 bp):
TCCTGAATGTTTCAACAGGGTCAAATGCCCCATGCATATTCCTGAACGTTTCAACAGGGTCGAAT
GCCCCATGCACGCTAA
Found at i:688773 original size:20 final size:20
Alignment explanation
Indices: 688748--688788 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
688738 TATCTTACCA
688748 TCATATCATACCCCATGGGT
1 TCATATCATACCCCATGGGT
688768 TCATATCATACCCCATGGGT
1 TCATATCATACCCCATGGGT
688788 T
1 T
688789 TAGCTTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (20 bp):
TCATATCATACCCCATGGGT
Found at i:697804 original size:17 final size:17
Alignment explanation
Indices: 697784--697817 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
697774 ATATCATTTA
697784 GGAATTTATATGCAGAT
1 GGAATTTATATGCAGAT
697801 GGAATTTATATGCAGAT
1 GGAATTTATATGCAGAT
697818 ACATACTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
GGAATTTATATGCAGAT
Found at i:698311 original size:4 final size:4
Alignment explanation
Indices: 698299--698344 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
698289 CACACACACA
* *
698299 TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG CATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
698345 CACATATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:715347 original size:14 final size:15
Alignment explanation
Indices: 715310--715348 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
715300 TGTCTTTTGT
715310 TCTTCTA-CTT-T-C
1 TCTTCTATCTTCTCC
715322 TCTTCTATCTTCTCC
1 TCTTCTATCTTCTCC
715337 TCTTC-ATCTTCT
1 TCTTCTATCTTCT
715349 TTATCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.29
13 3 0.12
14 8 0.33
15 6 0.25
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTTCTATCTTCTCC
Found at i:719257 original size:2 final size:2
Alignment explanation
Indices: 719220--719244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
719210 CAAATGAAAT
719220 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
719245 GATTGTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.